RetrogeneDB ID: retro_ecab_487

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:48707307..48707705(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015686
• Aliases: None
• Description: None

Sequence

>retro_ecab_487
ATTAGAGTATAAAAAGACTTGGTGAGAGGAATGGATGAACACAGTGAGAACTTCAACAAAGAGACAGAAAGTATAAGAAA
GTAAGAATAGAAGTCACAGAGGTGAAGAATACAATAACTGAACTGAAGAGTACGTGGGAGGGGCTCAATAGCAGACTAGG
CGAAGCAGGAGAAAGGACCAGTGAAATCGAAGACAAGGCAGCGGAACTCACCCAATCAGAGCACCAAAAGGAAAAAAGAA
TGAAAAAAAGTGAAGCCAGCTTCAGGGACTTATGGGACAACATCAAACAGACTAACACTTGCATTATAGGAGTCCCAGAA
GGAGAAGAGAGAGAGAAAGGGGCAGAAAACTTATTTGAAGAAATAATGGCTGAAAACTTCCCTAATCTGGGGAAGGAA

Alignment

ORF - retro_ecab_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.18 %
• Parental protein coverage: 77.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKMLTKLKRRMDEHSGNFNKETDSIRK-CQIEVTELKNTIPELTNTLEGFNSRLDEAEERISELNDRA-E
          I.....L.R.MDEHS.NFNKET.SIRK...IEVTE.KNTI.EL..T.EG.NSRL.EA.ER.SE..D.A.E
Retrocopy IRV*KDLVRGMDEHSENFNKETESIRK<VRIEVTEVKNTITELKSTWEGLNSRLGEAGERTSEIEDKAAE

Parental  LTQSEQQKEKRMKNTDNSLRELWDNIKHANIRIIGVPEGEERDKGAENLFVEIIQENFPNLRKE
          LTQSE............S.R.LWDNIK..N..IIGVPEGEER.KGAENLF.EI..ENFPNL.KE
Retrocopy LTQSEHXXXXXXXXXEASFRDLWDNIKQTNTCIIGVPEGEEREKGAENLFEEIMAENFPNLGKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	0.00 RPM
SRP021940_cerebellum	0.16 RPM	0.00 RPM
SRP021940_embryo	0.10 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_487 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_487 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015686	14 retrocopies	retro_ecab_1030, retro_ecab_1031, retro_ecab_1111, retro_ecab_1127, retro_ecab_207, retro_ecab_208, retro_ecab_326, retro_ecab_487 , retro_ecab_491, retro_ecab_518, retro_ecab_607, retro_ecab_625, retro_ecab_863, retro_ecab_881,